<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.3.0">
  <description>Get gene lists from a list of reactions and a GSMN.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
 -r "$reactionFile"
#if str($sep):
 -sep "$sep"
#end if
 $hasHeader
#if str($i) != 'nan':
 -col "$i"
#end if
 -o "$outputFile"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
    <param argument="-r" format="tsv" label="Input Reaction file" name="reactionFile" optional="false" type="data" value=""/>
    <param argument="-sep" label="Separator in reaction file" name="sep" optional="true" type="text" value="&#9;">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-header" checked="false" falsevalue="" label="Skip reaction file header" name="hasHeader" truevalue="-header" type="boolean" value="false"/>
    <param argument="-col" label="Column number in reaction file (first as 1)" name="i" optional="true" type="integer" value="1"/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputFile"/>
  </outputs>
  <tests>
    <test>
    <param name="sbml" value="XF_network.sbml"/>
    <param name="reactionFile" value="XF_network_R_Seed.tab"/>
    <output ftype="tsv" name="outputFile">
      <assert_contents>
        <has_n_lines n="2"/>
        <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
        <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
      </assert_contents>
    </output>
  </test>
  </tests>
  <help><![CDATA[Get associated gene list from a list of reactions and a GSMN. Parse GSMN GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
  <citations/>
</tool>